The Chromosome-Level Genome Assembly of Bean Blossom Thrips (<i>Megalurothrips usitatus</i>) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants
<i>Megalurothrips usitatus</i> (Bagnall) is a destructive pest of legumes, such as cowpea. The biology, population dynamics and control strategies of this pest have been well studied. However, the lack of a high-quality reference genome for <i>M. usitatus</i> has hindered the...
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MDPI AG
2023-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/14/11268 |
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| author | Zhijun Zhang Jiandong Bao Qizhang Chen Jianyun He Xiaowei Li Jiahui Zhang Zhixing Liu Yixuan Wu Yunsheng Wang Yaobin Lu |
| author_facet | Zhijun Zhang Jiandong Bao Qizhang Chen Jianyun He Xiaowei Li Jiahui Zhang Zhixing Liu Yixuan Wu Yunsheng Wang Yaobin Lu |
| author_sort | Zhijun Zhang |
| collection | DOAJ |
| description | <i>Megalurothrips usitatus</i> (Bagnall) is a destructive pest of legumes, such as cowpea. The biology, population dynamics and control strategies of this pest have been well studied. However, the lack of a high-quality reference genome for <i>M. usitatus</i> has hindered the understanding of key biological questions, such as the mechanism of adaptation to feed preferentially on high-protein host plants and the resistance to proteinase inhibitors (PIs). In this study, we generated a high-resolution chromosome-level reference genome assembly (247.82 Mb, 16 chromosomes) of <i>M. usitatus</i> by combining Oxford Nanopore Technologies (ONT) and Hi-C sequencing. The genome assembly showed higher proportions of GC and repeat content compared to other Thripinae species. Genome annotation revealed 18,624 protein-coding genes, including 4613 paralogs that were preferentially located in TE-rich regions. GO and KEGG enrichment analyses of the paralogs revealed significant enrichment in digestion-related genes. Genome-wide identification uncovered 506 putative digestion-related enzymes; of those, proteases, especially their subgroup serine proteases (SPs), are significantly enriched in paralogs. We hypothesized that the diversity and expansion of the digestion-related genes, especially SPs, could be driven by mobile elements (TEs), which promote the adaptive evolution of <i>M. usitatus</i> to high-protein host plants with high serine protease inhibitors (SPIs). The current study provides a valuable genomic resource for understanding the genetic variation among different pest species adapting to different plant hosts. |
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| language | English |
| last_indexed | 2024-03-11T01:01:51Z |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-9b4e86f3197744bca440cf24a66e73c12023-11-18T19:36:41ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-07-0124141126810.3390/ijms241411268The Chromosome-Level Genome Assembly of Bean Blossom Thrips (<i>Megalurothrips usitatus</i>) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host PlantsZhijun Zhang0Jiandong Bao1Qizhang Chen2Jianyun He3Xiaowei Li4Jiahui Zhang5Zhixing Liu6Yixuan Wu7Yunsheng Wang8Yaobin Lu9State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaHunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410125, ChinaState Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China<i>Megalurothrips usitatus</i> (Bagnall) is a destructive pest of legumes, such as cowpea. The biology, population dynamics and control strategies of this pest have been well studied. However, the lack of a high-quality reference genome for <i>M. usitatus</i> has hindered the understanding of key biological questions, such as the mechanism of adaptation to feed preferentially on high-protein host plants and the resistance to proteinase inhibitors (PIs). In this study, we generated a high-resolution chromosome-level reference genome assembly (247.82 Mb, 16 chromosomes) of <i>M. usitatus</i> by combining Oxford Nanopore Technologies (ONT) and Hi-C sequencing. The genome assembly showed higher proportions of GC and repeat content compared to other Thripinae species. Genome annotation revealed 18,624 protein-coding genes, including 4613 paralogs that were preferentially located in TE-rich regions. GO and KEGG enrichment analyses of the paralogs revealed significant enrichment in digestion-related genes. Genome-wide identification uncovered 506 putative digestion-related enzymes; of those, proteases, especially their subgroup serine proteases (SPs), are significantly enriched in paralogs. We hypothesized that the diversity and expansion of the digestion-related genes, especially SPs, could be driven by mobile elements (TEs), which promote the adaptive evolution of <i>M. usitatus</i> to high-protein host plants with high serine protease inhibitors (SPIs). The current study provides a valuable genomic resource for understanding the genetic variation among different pest species adapting to different plant hosts.https://www.mdpi.com/1422-0067/24/14/11268<i>Megalurothrips usitatus</i>bean blossom thripschromosome-level genome assemblyparalogprotein digestion-related geneslegumes |
| spellingShingle | Zhijun Zhang Jiandong Bao Qizhang Chen Jianyun He Xiaowei Li Jiahui Zhang Zhixing Liu Yixuan Wu Yunsheng Wang Yaobin Lu The Chromosome-Level Genome Assembly of Bean Blossom Thrips (<i>Megalurothrips usitatus</i>) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants International Journal of Molecular Sciences <i>Megalurothrips usitatus</i> bean blossom thrips chromosome-level genome assembly paralog protein digestion-related genes legumes |
| title | The Chromosome-Level Genome Assembly of Bean Blossom Thrips (<i>Megalurothrips usitatus</i>) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants |
| title_full | The Chromosome-Level Genome Assembly of Bean Blossom Thrips (<i>Megalurothrips usitatus</i>) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants |
| title_fullStr | The Chromosome-Level Genome Assembly of Bean Blossom Thrips (<i>Megalurothrips usitatus</i>) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants |
| title_full_unstemmed | The Chromosome-Level Genome Assembly of Bean Blossom Thrips (<i>Megalurothrips usitatus</i>) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants |
| title_short | The Chromosome-Level Genome Assembly of Bean Blossom Thrips (<i>Megalurothrips usitatus</i>) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants |
| title_sort | chromosome level genome assembly of bean blossom thrips i megalurothrips usitatus i reveals an expansion of protein digestion related genes in adaption to high protein host plants |
| topic | <i>Megalurothrips usitatus</i> bean blossom thrips chromosome-level genome assembly paralog protein digestion-related genes legumes |
| url | https://www.mdpi.com/1422-0067/24/14/11268 |
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